Trees under the microscope

[Gary Prentice]

I'm sorry to hear that it's not working. Did you buy it second-hand? What make and model is it? It really shouldn't be hard to operate, when I got mine I didn't even look at the manual, just plugged it in and put the mini CD in and it worked right away. Mine has a video function too but I just use it as a CCTV till i line up the right shot for a still.

 

I got it sorted after posting, so I'm now able to take pictures. I need to mess about a bit more with it but I don't think its going to do the sort of things I would like to do. In that it won't magnify to the extent I'd like - I really want to be seeing cells:lol:

 

I was hoping someone would help me with this too. When I get a moment I plan to put some pictures up of a simple slide being produced from non-woody material using an improvised microtome. But my own wood ones have been a bit poor, I could do with advice

 

First you'd have to explain 'microtome' I'll look it up! Maybe Tony knows a bit more?

[daltontrees]

I got it sorted after posting, so I'm now able to take pictures. I need to mess about a bit more with it but I don't think its going to do the sort of things I would like to do. In that it won't magnify to the extent I'd like - I really want to be seeing cells:lol:

 

I was hoping someone would help me with this too. When I get a moment I plan to put some pictures up of a simple slide being produced from non-woody material using an improvised microtome. But my own wood ones have been a bit poor, I could do with advice

 

First you'd have to explain 'microtome' I'll look it up! Maybe Tony knows a bit more?

 

Good to hear it's working better. But if you want to see cells you will almost certainly not do this with a reflected light microscope and you may have to take the leap to transmitted light microscopy (see my earlier posts)

 

Microtomes are simple in principle. They hold samples firmly while very very thin slices are taken of them. Bear with me and I will post a few pictures. You should be able to improvise a microtome with a bolt, two nuts, a razor blade and a candle.

[Gary Prentice]

Good to hear it's working better. But if you want to see cells you will almost certainly not do this with a reflected light microscope and you may have to take the leap to transmitted light microscopy (see my earlier posts)

 

Microtomes are simple in principle. They hold samples firmly while very very thin slices are taken of them. Bear with me and I will post a few pictures. You should be able to improvise a microtome with a bolt, two nuts, a razor blade and a candle.

 

I've been looking at some transmitted light microscopes and have got a little lost amongst the options. I think I'd prefer a stereo? type (I don't know why really) but still linked or with the ability to be linked to the computer.

 

If I can find something, could I PM you for further advice i.e yea or nay on the purchase?

[daltontrees]

Happy to help, PM me when you have lined up a victim.

 

Stereo aint quite the right word, it suggests that you will be able to discern depth in the subject such that it looks three dimensional. The right word is probably binocular. Two identical eyepieces having the same view. Some find it easier on the eyes because you don't have to close one eye.

 

There is also the option of a trinocular. These aren't cheap though. I'm not suggesting anyone has three eyes, what they are good for is keeping a camera or computer connection attached to one of them semi-permanently so that when you see something interesting you can instantly take a picture of it.

 

I was going to get on to the subject of photographing through the microscope shortly. But basically if you have any microscope that has a 23mm or 30mm sleeve for the eyepiece, you have lots of options. Therefore don't get any instrument that doesn't have a slide-out detachable eyepiece.

 

And if you get a microscope, I will give you a couple of tree slides that I have duplicates of. By then I should have posted how to make your own microtome and then your own slides. Then you can dissect some branch unions and make slides and solve the riddle once and for all. Should have it wrapped up by Easter. You weren't doing anything else, were you?

[daltontrees]

Another quick tutorial for anyone that's interested. This is a bit hardcore but is useful foundation understanding for anyone that wants to get into microscopy.

 

So far I have referred to the two types of microscope being reflected and transmitted light. I am going to concentrate on transmitted light for now. That's basically looking at light passing through thin sections. But whadya know there is more than one kind of light.

 

Every bit of light we receive is made up of zillions of photons, little bundles of light energy. Each one has a random orientation or plane. So say you were looking at a conventional wrist watch. One photon could be arriving in your eye in the 12 o'clock 6 o'clock plane. Another in the 2 o'clock 8 o'clock plane. Yet another in the 11.30 5.30 plane etc etc a million times over in absolutely every possible plane. The eye can't tell which plane each photon is in, it doesn't matter, it's all just light.

 

But white light is made up of all the colours at once. Proof of this is that it can be split by a prism. Dig out a copy of Dark Side of the Moon by Pink Floyd, that's what's on the cover.

 

When you look at white light through a microscope this is what you get. All colours and all orientations. This is called 'Bright Field'.

 

There are times, though, when you might only want to get one colour of light. For this, microscopes can be fitted with colour filters. Easy.

 

The next bit is a bit more complicated. Sometimes you only want light in one plane of orientation. I will explain why in a minute. Say you only want light in the 12 - 6 plane. This is what polarising filters do. They have a very very fine set of lines on them that only lets those photons through that are in the right plane of orientation. Like say if you stood over a road drain with slats on it and dropped a packet of uncooked spaghetti onto it in random orientations. Only the spaghetti that was in the same orientation as the grating would get through. The rest would bounce off. This is what a polarising filter is doing, only the photons in one plane are getting through. Looking at a slide in this light is called 'Plane Polarised'.

 

With me so far? The polarising filter goes between the lamp and the slide so the slide is only getting polarised light through it.

 

What would happen if you put another polarising filter over the slide at right angles to the first one. That's right, no light can get through. Like 2 drain covers. What one lets through the other catches.

 

But that's not strictly true. Whatever is between them could be acting like a mini prism, in effect rotating the photons slightly. Thus a few make it through the second polariser because their plane of orientation is no longer at right angles to the second polariser. Doing this is called looking in 'Cross Polarised Light'.

 

OK I am going to find a picture of a rock thin section to illustrate why this is useful.

[daltontrees]

OK I have found something suitable. A thin section of a piece of mica-rich granite, I think. In the middle is a crystal of Biotite, a mica. In a rock this looks jet black in reflected light. In thin section it is transparent and slightly yellow/green/brown. The picture is in Plane Polarised Light.

 

The second picture is in Cross Polarised Light. No light should be getting through, but it is because every crystal is rotating the light. The biotite is no brightly coloured. The textureless grey stuff is quartz, all shades of grey depending on optic axis (never mind that bit).

 

OK now I need to find pics of a tree section in Cross Polarised Light.

[daltontrees]

I have the very thing here. I can't remember what it is, a thin section of a cross section of a broadleaf tree. Individual cells can clearly be seen. The magnification is 600x, so much so that even though the thin section is only about 1/200th of a millimetre I was unable to focus on the front and the back of the thin section at the same time. It looks blurry because you are seeing one side of the slide out of focus and the other in focus. The first picture is in Plane Polarised Light. The S1, S2 and S3 layers of the cell walls are visible.

 

The second slide shows it in Cross Polarised Light. Sure enough, where there is nothing to rotate the light it looks black. But the cellulose in the cell walls, especially the shallow angled cellulose in S2, is diffracting the light so that it is getting through the second polariser. And if it had been infected with say K. deusta in soft rot mode, you would have been able to see a reduction in cellulose. Which is what I am trying to put across as the great benefits of microscopy with the advantage of Cross Polarised Light and a rotating stage.

 

To be honest I don't see how anyone could get by without one!

[Gary Prentice]

Happy to help, PM me when you have lined up a victim.

 

Stereo aint quite the right word, it suggests that you will be able to discern depth in the subject such that it looks three dimensional. The right word is probably binocular. Two identical eyepieces having the same view. Some find it easier on the eyes because you don't have to close one eye.

 

There is also the option of a trinocular. These aren't cheap though. I'm not suggesting anyone has three eyes, what they are good for is keeping a camera or computer connection attached to one of them semi-permanently so that when you see something interesting you can instantly take a picture of it.

 

I was going to get on to the subject of photographing through the microscope shortly. But basically if you have any microscope that has a 23mm or 30mm sleeve for the eyepiece, you have lots of options. Therefore don't get any instrument that doesn't have a slide-out detachable eyepiece.

 

And if you get a microscope, I will give you a couple of tree slides that I have duplicates of. By then I should have posted how to make your own microtome and then your own slides. Then you can dissect some branch unions and make slides and solve the riddle once and for all. Should have it wrapped up by Easter. You weren't doing anything else, were you?

 

I apologise, but it was early and I couldn't think at the time how to spell binocular:blushing: In my defence though I think I've seen some advertised as such:thumbup:

 

I wouldn't need to wrap up the riddle by Easter, as the personal project has a later deadline (not that I'm sure I want to get involved in that debate too much), but the thoughts appreciated.

 

Anyway, it's all given me more idea of what I'm looking at, thank you.

[daltontrees]

I apologise, but it was early and I couldn't think at the time how to spell binocular:blushing: In my defence though I think I've seen some advertised as such:thumbup:

 

I wouldn't need to wrap up the riddle by Easter, as the personal project has a later deadline (not that I'm sure I want to get involved in that debate too much), but the thoughts appreciated.

 

Anyway, it's all given me more idea of what I'm looking at, thank you.

 

I meant that YOU would have solved the riddle by Easter. Go for it, that's what I say. If you have an inquiring mid that imagines the way trees work at a cellular level, seeing them at a cellular level with the use of a microscope takes you right into that world. You don't need to be Alice in Wonderland to appreciate how liberating it can be to take a stroll amongst the xylem.

[Gary Prentice]

Jules I have a book on my shelf that may be of interest. Field and Laboratory Guide to Tree Pathology by R O Blanchard and T A Tattar. It's an old one but discusses staining and fixing and so forth. My missus saw it on ebay and it was about trees so she bought it.

 

 

http://www.ebay.co.uk/itm/Field-and-Laboratory-Guide-to-Tree-Pathology-Robert-O-Blanchard-/191029974934?pt=Non_Fiction&hash=item2c7a461796 I didn't pay that much, about a fiver or so. I can pop my copy in the post if it's of interest.

Edited January 15, 2014 by Gary Prentice